cgpu’s gists

cgpu / finddups.nf

Created June 16, 2021 02:05 — forked from lindenb/finddups.nf

workflow nextflow finding duplicated files and creating a bash script to replace the duplicate with a symbolic link

cgpu / packer-nextflow.yaml

Created March 17, 2021 20:50 — forked from alanbchristie/packer-nextflow.yaml

An example of a Nextflow Packer file in YAML

	---

	# Packer machine image configuration for a Nextflow/Docker machine.
	#
	# To use this file (Packer expects a JSON file) you need to
	# use the project's yaml2json module to convert it to JSON.
	# From this directory and a Suitable Python (see root's requirements.txt)
	# you can run...
	#
	# ../../../yaml2json.py < nextflow.yml > nextflow.json

cgpu / sra-paired.sh

Created May 1, 2020 22:59 — forked from slowkow/sra-paired.sh

Check if an SRA file contains paired-end data.

	#!/usr/bin/env bash
	# sra-paired.sh
	# Kamil Slowikowski
	# April 23, 2014
	#
	# Check if an SRA file contains paired-end sequencing data.
	#
	# See documentation for the SRA Toolkit:
	# http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump

cgpu / read-multiple-csv-files.R

Created April 29, 2020 22:31 — forked from apreshill/read-multiple-csv-files

Read multiple csv files into R

	# stack overflow answer from Joran Ellis:
	# http://stackoverflow.com/questions/5319839/read-multiple-csv-files-into-separate-data-frames

	# If the path is different than your working directory
	# you'll need to set full.names = TRUE to get the full
	# paths.
	my_files <- list.files("path/to/files")

	# Further arguments to read.csv can be passed in ...
	all_csv <- lapply(my_files,read.csv,...)

cgpu / get_content.groovy

Created April 19, 2020 14:36 — forked from kdabir/get_content.groovy

get content from url and write to a file in groovy

	// saving from url to a file (append)
	new File("output.xml") << new URL ("http://some.url/some/path.xml").getText()

cgpu / papermill_python_api.py

Created March 1, 2020 22:44 — forked from GabrielSGoncalves/papermill_python_api.py

executing papermill using its Python API

	import papermill as pm

	pm.execute_notebook('weather_forecast_using_pyowm.ipynb',
	'weather_forecast_using_pyowm_output.ipynb',
	parameters={'city':'Sao Paulo,BR'},
	kernel_name='papermill-tutorial')

cgpu / print_progress.R

Created February 16, 2020 23:26 — forked from jilmun/print_progress.R

	# print everything after loop is finished
	for (i in 0:101) {
	print(i)
	Sys.sleep(0.01)
	}

	# simplist way to print within loop
	for (i in 0:101) {
	print(i)
	Sys.sleep(0.01)

cgpu / plink_pruning_prep.sh

Created November 27, 2019 17:14 — forked from janxkoci/plink_pruning_prep.sh

This simple script prepares your VCF dataset for pruning with Plink. It takes name of the input VCF as argument and produces new, annotated VCF.

	#!/bin/bash

	# SCRIPT USAGE:
	# bash plink_pruning_prep.sh filtered_snp_file.vcf

	# REQUIREMENTS:
	# This script uses several software packages, all available from [Bioconda channel](https://bioconda.github.io/).
	# They can be installed with simple:
	# conda install tabix bcftools plink

cgpu / KaplanMeierPlotR.R

Created October 24, 2019 18:46 — forked from nbremer/KaplanMeierPlotR.R

Creating a Kaplan Meier plot, used in Survival Analysis, using R's ggplot2 package

	#' Create a Kaplan-Meier plot using ggplot2
	#'
	#' @param sfit: a survfit object
	#' @param table: logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
	#' @param returns logical: if TRUE, return an arrangeGrob object
	#' @param xlabs: x-axis label
	#' @param ylabs: y-axis label
	#' @param ystratalabs: The strata labels. Default = levels(summary(sfit)$strata)
	#' @param ystrataname: The legend name. Default = "Strata"
	#' @param timeby numeric: control the granularity along the time-axis

cgpu / gist:6b15bc8af08ba319c8fd793e5c07f789

Created October 16, 2019 20:46 — forked from rxaviers/gist:7360908

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